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HMRI Report Summary

Project ID: 616905
Funded under: FP7-IDEAS-ERC
Country: Germany

Periodic Report Summary 2 - HMRI (Non-Invasive In-Vivo Histology in Health and Disease Using Magnetic Resonance Imaging (MRI))

The hMRI project develops and applies novel non-invasive magnetic resonance imaging (MRI) methods to reliably characterize the detailed anatomical microstructure of the human cortex. The first phase of this project was focused on the development of MRI data acquisition, data analysis methods and biophysical models, in order to enable the (clinical) neuroscience experiments in the second phase.

We achieved imaging of the human cortex using quantitative multi-parameter maps (MPMs) with an unprecedented 400 µm isotropic resolution. This was only possible by developing and seamlessly integrating optical prospective motion correction, which addresses the unavoidable head motion artifacts at such high spatial resolution. The MPMs are combined with cutting edge diffusion imaging to estimate features of the cortical microstructure such as fiber densities or myelination. In addition to improved data acquisition methods, diffusion imaging is further improved by leveraging the potential of the recently commissioned 3T Connectom MRI at the MPI for Human Cognitive and Brain Sciences, which offers the highest gradient amplitude (300 mT/m) for human imaging and is one of just three systems world wide (

We have developed novel biophysical models that integrate the high-resolution MRI data by combining information from different MRI contrasts. The developments include a specialized model of the diffusion contrast in the cortex. It combines information about diffusion with macroscopic cortical features to improve the inference of tangential and radial fibers in the cortex, which play a central role in cortical information processing. We also developed a linear relaxometry model that combines multiple contrasts and describes the inter-relation of different physical relaxation mechanisms in the brain tissue. It can be used to characterize the brain microstructure, reduce the scan time, increase image quality and even synthesize quantitative parameter maps by exploiting the known interrelation.

Post-mortem MRI and histology were further developed and applied in order to inform model building and validate the models. We have pushed the limits of current post-mortem histology methods, which are limited by the vagaries of staining efficiency and their 2D view on the brain anatomy. Tissue clearing combined with advanced microscopy and image processing methods allowed for comprehensive imaging of cortical structures. By using proton-induced X-ray emission (PIXE) and mass spectroscopy imaging we were able to estimate high-resolution maps (from macroscopic- down to cellular resolution) of iron and myelination in the brain. These methods allow for careful quantitative validation of biophysical models and provide important information about the cortical microstructure.

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